2010 Collaborative Research: Integrating the Unknown-eome with Abiotic Stress Response Networks in Arabidopsis

长期目标和背景：本研究项目的长期目标是促进拟南芥中每个基因的功能分配。到目前为止，超过20%的植物基因编码的蛋白质的功能是完全未知的，其中高达43%的蛋白质的功能特征很差。这项研究的重点是未知功能的基因和对环境胁迫(如低温、干旱、盐分、洪水、强光和氧化环境)做出反应的网络。环境压力是世界范围内农作物损失的主要原因。植物的生存和生长取决于其应对环境压力的能力。很明显，植物的逆境反应是基因网络和新陈代谢一系列复杂变化的结果。虽然数以千计的基因与压力网络有关，但在少数情况下，它们的生化和遗传功能已被阐明。事实上，到目前为止发现的大多数逆境调节基因都具有完全未知的功能(S)。具体目标和预期结果：1.确定1,600个功能未知基因表达中断的植物品系的逆境耐性变化。该方法是测试植物品系对包括缺水、盐分、强光、高温、冷藏、冷冻、厌氧、重金属和氧化胁迫在内的胁迫的抗性或敏感性。主要目标是开始一种系统的方法来评估所有拟南芥基因对逆境耐受性的贡献。预期结果：为1,600个功能未知的基因分配一个假定的功能。确定全球蛋白质相互作用网络中功能未知的基因之间的关系。该方法是使用随机酵母双杂交筛选策略确定20,000个蛋白质-蛋白质相互作用的例子。主要目标是发现已知和未知功能的基因之间的联系。预期结果：拟南芥的蛋白质-蛋白质图谱。在植物中过度表达150个功能未知的选定基因，测试转基因植物的抗逆性变化，并寻找相互作用的蛋白质伙伴。对每个基因进行检验的假设是，它的过度表达可以改变特定的应激反应。预期结果：确定在应激反应中具有中心重要性的未知功能蛋白质及其蛋白质伙伴。在至少两种不同胁迫条件下生长的20个胁迫反应突变体的基因表达谱变化。主要目标是开始创建一个基因表达变化网络，以帮助更好地专注于对环境压力具有潜在重要性的酶和调节器的深入实验。预期结果：确定与环境压力有关的基因网络。协调一个关于拟南芥未知功能基因(“未知基因”)信息的中央网站，并就科学在农业、环境和人类健康方面的作用，为处于特权地位和在科学中代表性不足的人提供外联和培训活动。将建立基于网络的资源，以传播未公布的信息，并将注释和数据链接到所有的拟南芥“未知数”。该项目的所有工厂线路和成果将每两年向学术界发布一次。预期结果：建立一个加强未知功能基因研究的集中网站。广泛影响：拟议研究的两个关键的“更广泛的影响”是：1)开发和维护一个关于功能未知的拟南芥基因信息的集中网站。该网站将跟踪和传播“未知”基因纯合子T-DNA插入线及其表型的信息，并提供基因结构、基因注释、蛋白质相互作用和信使核糖核酸图谱数据。2)K-12教育外展和对博士后、研究生和本科生实习生的跨学科培训。暑期外展工作坊将向高中生传授关于拟南芥的孟德尔遗传、科学在农业、环境和人类健康中的作用。这个以实验室为基础的实习计划将提供建立自信的经历，并让学生接触到实验室和科学家。本科生和K-12的外展和培训活动都将针对在科学界处于弱势和代表性不足的人

Long-Term Goal and Background:The long-term goal of this research project is to facilitate the assignment of function to every gene in Arabidopsis thaliana. To date, the function of the proteins encoded by more than 20% of plant genes is completely unknown, with the function of up to 43% of these proteins poorly characterized. The specific focus of this research is genes of unknown function and the networks that respond to environmental stress, such as chilling, drought, salt, flooding, high light, and oxidative environments. Environmental stress is the primary cause of crop loss world-wide. A plant's survival and growth is dependent on its ability to cope with environmental stresses. It is clear that a plant's stress response results from a complex set of changes in gene networks and metabolism. While 1000s of genes have been linked to stress networks, in only a few cases have their biochemical and genetic functions been elucidated. In fact, most of the stress-regulated genes identified to date have completely unknown function(s).Specific Aims and Expected Outcome:1. Determine the change in stress tolerance for 1,600 plant lines with a disrupted expression of genes of unknown function. The approach is to test plant lines for resistance or susceptibility to stresses including water deficit, salt, high light, heat, chilling, freezing, anaerobiosis, heavy metal and oxidative stress. The primary goal is to begin a systematic approach to evaluate the contribution of all Arabidopsis genes to stress tolerance. Expected outcome: Assigning a putative function to 1,600 genes with an unknown function.2. Determine the relationship of genes of unknown function within a global protein-proteininteraction network. The approach is to determine 20,000 examples of protein-protein interactions using a random yeast two-hybrid screening strategy. The primary goal is to uncover links between genes of known and unknown function. Expected outcome: A protein-protein map for Arabidopsis.3. Over-express 150 selected genes of unknown function in plants, test transgenic plants for changes in stress tolerance, and search for interacting protein partners. The hypothesis to be tested for each gene is that its over-expression can alter a particular stress response. Expected outcome: Identifying proteins of unknown function with a central importance in stress response and their protein partners.4. Profile changes in gene expression in 20 stress-response mutants grown under at least two different stress conditions. The primary goal is to begin creating a network of gene expression changes that can help better focus in-depth experiments on enzymes and regulators of potential importance to environmental stress. Expected outcome: Identifying gene networks involved in environmental stress.5. Coordinate a centralized website for information on genes of unknown function ("unknowns")from Arabidopsis and provide outreach and training activities for those under privileged andunderrepresented in science, on the role of science in agriculture, the environment, and human health. Web-based resources will be established to disseminate unpublished information and link annotation and data to all Arabidopsis "unknowns". All plant lines and results of the project will be released to the academic community on a biannual basis. Expected outcome: A centralized website to enhance research on genes with unknown function.Broader Impacts:The two key "Broader Impacts" of the proposed research are: 1) development and maintenance of a centralized website for information on Arabidopsis genes of unknown function. This site will track and disseminate information on homozygous T-DNA insertion lines for "unknown" genes and their phenotypes, and provide gene structure, gene annotation, protein interaction and mRNA profiling data. 2) Educational outreach for K-12 and interdisciplinary training to postdoctoral, graduate and undergraduates trainees. A summer outreach workshop will teach high school students about Mendelian inheritance in Arabidopsis, the role of science in agriculture, the environment, and human health. This laboratory-based internship program will provide self-confidence building experiences and expose thestudents to laboratories and scientists. Both undergraduate and K-12 outreach and training activities will target the under privileged and underrepresented in science